Publications by Dr. Ramses van Zon

 
 

  1. Cybersecurity Training for Users of Remote Computing
    M. Ponce and R. van Zon
    Journal of Computational Science Education (accepted, 2023)
    [preprint] [pdf]
  2. Software-Enhanced Teaching and Visualization Capabilities of an Ultra-High-Resolution Video Wall
    R. van Zon and M. Ponce
    PEARC '19: Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning), Article No. 120, Pages 1–4 (2019)
    [doi:10.1145/3332186.3333149] [pdf]
  3. Deploying a Top-100 Supercomputer for Large Parallel Workloads: the Niagara Supercomputer
    M. Ponce, R. van Zon, S. Northrup, D. Gruner, J. Chen, F. Ertinaz, A. Fedoseev, L. Groer, F. Mao, B.C. Mundim, M. Nolta, J. Pinto, M. Saldarriaga, V. Slavnic, E. Spence, C.-H. Yu and W.R. Peltier
    PEARC ’19: Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (Learning), Article No. 34 (8 pages) (2019)
    [https://dl.acm.org/doi/pdf/10.1145/3332186.3332195] [pdf]
  4. Trends in Demand, Growth, and Breadth in Scientific Computing Delivered by a High-Performance Computing Center
    R. van Zon, M. Ponce, E. Spence and D. Gruner
    Journal of Computational Science Education 10 (1), 53–60 (2019)
    [doi:10.22369/issn.2153-4136/10/1/9] [pdf]
  5. Scientific Computing, High-Performance Computing and Data Science in Higher Education
    M. Ponce, E. Spence, R. van Zon and D. Gruner
    Journal of Computational Science Education 10 (1), 24–31 (2019)
    [doi:10.22369/issn.2153-4136/10/1/5] [pdf]
  6. Bridging the Gap between Emerging and Established Scientific Computing Disciplines
    M. Ponce, E. Spence, D. Gruner and R. van Zon
    Journal of Computational Science Education 10 (1), 4–11 (2019)
    [doi:10.22369/issn.2153-4136/10/1/1] [pdf]
  7. Object-oriented scientific programming without reinventing the wheel
    R. van Zon
    Book review for Book review for “ Scientific Software Design, The Object-Oriented Way” by D. Rouson et al.; Computing In Science and Engineering 14 5-6 (2012)
    [doi:10.1109/MCSE.2012.6] [pdf]
  8. Free energy landscape of protein-like chains with discontinuous potentials
    H. Bayat Movahed, R. van Zon and J. Schofield
    Journal of Chemical Physics 136 245103 (13 pages) (2012)
    [doi:10.1063/1.4729850] [pdf]
  9. Mapping quantum-classical Liouville equation: Projectors and trajectories
    A. Kelly, R. van Zon, J. Schofield and R. Kapral
    Journal of Chemical Physics 136, 084101 (14 pages) (2012)
    [doi:10.1063/1.3685420] [pdf]
  10. SciNet: Lessons Learned from Building a Power-efficient Top-20 System and Data Centre
    C. Loken, D. Gruner, L. Groer, W. R. Peltier, N. Bunn, M. Craig, T. Henriques, J. Dempsey, C.-H. Yu, J. Chen, L. J. Dursi, J. Chong, S. Northrup, J. Pinto, N. Knecht and R. van Zon
    in “High Performance Computing Symposium (HPCS2010),” Journal of Physics: Conference Series 256, 012026 (36 pages) (2010)
    [doi:10.1088/1742-6596/256/1/012026] [pdf]
  11. Constructing smooth potentials of mean force, radial distribution functions, and probability densities from sampled data
    R. van Zon and J. Schofield
    Journal of Chemical Physics 132, 154110 (13 pages) (2010)
    [doi:10.1063/1.3366523] [pdf]
  12. Effective pair potentials for spherical nanoparticles
    R. van Zon
    Journal of Statistical Mechanics: Theory and Experiment (2009) P02008 (31 pages) (2009).
    [doi:10.1088/1742-5468/2009/02/P02008] [pdf]
  13. Quantum free energy differences from non-equilibrium path integrals: II. Convergence for the harmonic oscillator
    R. van Zon, L. Hernández de la Peña, G. Peslherbe and J. Schofield
    Physical Review E 78, 041104 (14 pages) (2008)
    [doi:10.1103/PhysRevE.78.041104] [pdf]
  14. Quantum free energy differences from non-equilibrium path integrals: I. Methods and application
    R. van Zon, L. Hernández de la Peña, G. Peslherbe and J. Schofield,
    Physical Review E 78, 041103 (11 pages) (2008)
    [doi:10.1103/PhysRevE.78.041103] [pdf]
  15. Event-driven dynamics of rigid bodies interacting via discretized potentials
    R. van Zon and J. Schofield
    Journal of Chemical Physics 128, 154119 (9 pages) (2008)
    [doi:10.1063/1.2901173] [pdf]
  16. Gaussian approximation to single particle correlations at and below the picosecond scale for Lennard-Jones and nanoparticle fluids
    R. van Zon, S.S. Ashwin and E.G.D. Cohen
    Nonlinearity 21 (5), R119–R137 (2008)
    [doi:10.1088/0951-7715/21/5/R01] [pdf]
  17. Efficient algorithms for rigid body integration using optimized splitting methods and exact free rotational motion
    R. van Zon, I.P. Omelyan and J. Schofield
    Journal of Chemical Physics 128, 136102 (2 pages) (2008)
    [doi:10.1063/1.2889937] [pdf]
  18. Symplectic algorithms for simulations of rigid body systems using the exact solution of free motion
    R. van Zon and J. Schofield
    Physical Review E 75, 056701 (5 pages) (2007)
    [doi:10.1103/PhysRevE.75.056701] [pdf]
  19. Discontinuous molecular dynamics for rigid bodies: Applications
    L. Hernández de la Peña, R. van Zon, J. Schofield and S.B. Opps
    Journal of Chemical Physics 126, 074106 (12 pages) (2007).
    [doi:10.1063/1.2434959] [pdf]
  20. Discontinuous molecular dynamics for semi-flexible and rigid bodies
    L. Hernández de la Peña, R. van Zon, J. Schofield and S.B. Opps
    Journal of Chemical Physics 126, 074105 (13 pages) (2007)
    [doi:10.1063/1.2434957] [pdf]
  21. Numerical implementation of the exact dynamics of free rigid bodies
    R. van Zon and J. Schofield
    Journal of Computional Physics 225, 145–164 (2007)
    [doi:10.1016/j.jcp.2006.11.019] [pdf]
  22. Short-time fluctuations of displacements and work
    R. van Zon, S.S. Ashwin and E.G.D. Cohen
    Comptes Rendus Physique 8, 633–640 (2007)
    [doi:10.1016/j.crhy.2007.05.011] [pdf]
  23. Stationary state fluctuation theorems for driven Langevin systems
    E.G.D. Cohen and R. van Zon
    Comptes Rendus Physique 8, 507–517 (2007)
    [doi:10.1016/j.crhy.2007.04.009] [pdf]
  24. Theorem on the distribution of short-time single particle displacements
    R. van Zon and E.G.D. Cohen
    Physica A 365, 108–112 (2006)
    [doi:10.1016/j.physa.2006.01.035] [pdf]
  25. Theorem on the distribution of short-time particle displacements with physical applications
    R. van Zon and E.G.D. Cohen,
    Journal of Statistical Physics 123, 1–37 (2006)
    [doi:10.1007/s10955-006-9027-9] [pdf]
  26. Mode-coupling theory for multiple-time correlation functions of tagged particle densities and dynamical filters designed for glassy systems
    R. van Zon and J. Schofield
    Journal of Physical Chemistry B 109, 21425–21436 (2005).
    [doi:10.1021/jp052234g] [pdf]
  27. Glassy dynamics and domains: Explicit results for the East model
    R. van Zon and J. Schofield
    Journal of Chemical Physics 122, 194502 (2005)
    [doi:10.1063/1.1897372] [pdf]
  28. Work and Heat Fluctuations in Systems with Deterministic and Stochastic Forces
    E. G. D. Cohen and R. van Zon
    Complexity, Metastability and Nonextensivity (C. Beck, A. Rapisarda and C. Tsallis eds.), pp. 3-12 (World Scientific, 2005)
    [doi:10.1142/9789812701558_0001]
  29. Non-equilibrium Thermodynamics and Fluctuations
    R. van Zon and E. G. D. Cohen
    Physica A 340 (1-3), 66-75 (2004)
    [doi:10.1016/j.physa.2004.03.078] [pdf]
  30. Extended Heat-Fluctuation Theorems for a System with Deterministic and Stochastic Forces
    R. van Zon and E. G. D. Cohen
    Physical Review E 69, 056121 (2004)
    [doi:10.1103/PhysRevE.69.056121] [pdf]
  31. Power and Heat Fluctuation Theorems for Electric Circuits
    R. van Zon, S. Ciliberto and E. G. D. Cohen
    Physical Review Letters 92, 130601 (2004)
    [doi:10.1103/PhysRevLett.92.130601] [pdf]
  32. Extension of the Fluctuation Theorem
    R. van Zon and E. G. D. Cohen
    Physical Review Letters 91, 110601 (2003)
    [doi:10.1103/PhysRevLett.91.110601] [pdf]
  33. Transient and Stationary Work-Fluctuation Theorems for a Dragged Brownian Particle
    R. van Zon and E. G. D. Cohen
    Physical Review E 67, 046102 (2003)
    [doi:10.1103/PhysRevE.67.046102] [pdf]
  34. Front Propagation Techniques to Calculate the Largest Lyapunov Exponent of Dilute Hard Disk Gases
    R. van Zon and H. van Beijeren
    Journal of Statistical Physics 109 (3-4) 641-669 (2002)
    [doi:10.1023/A:1020414615453] [pdf]
  35. Pairing of Lyapunov Exponents for a Hard-Sphere gas under Shear in the Thermodynamic Limit
    D. Panja and R. van Zon
    Physical Review E 66, 021101 (2002)
    [doi:10.1103/PhysRevE.66.021101] [pdf]
  36. Lyapunov Exponent Pairing for a Thermostatted Hard-Sphere Gas under Shear in the Thermodynamic Limit
    D. Panja and R. van Zon
    Physical Review E 65, 060102(R) (2002)
    [doi:10.1103/PhysRevE.65.060102] [pdf]
  37. Multiple-Point and Multiple-Time Correlations Functions in a Hard-Sphere Fluid
    R. van Zon and J. Schofield
    Physical Review E 65, 011107 (2002)
    [doi:10.1103/PhysRevE.65.011107] [pdf]
  38. Mode Coupling Theory for Multiple-Point and Multiple-Time Correlation Functions
    R. van Zon and J. Schofield
    Physical Review E 65, 011106 (2002)
    [doi:10.1103/PhysRevE.65.011106] [pdf]
  39. Kinetic Theory Estimates for the Kolmogorov-Sinai Entropy and the Largest Lyapunov Exponents for Dilute, Hard-Ball Gases and for Dilute, Random Lorentz Gases
    R. van Zon, H. van Beijeren and J. R. Dorfman
    Hard Ball Systems and the Lorentz Gas (D. Szasz ed.), Encyclopaedia Math. Sci. 101, 231-278 (Springer, Berlin, 2000)
    [doi:10.1007/978-3-662-04062-1_10] [pdf]
  40. Kinetic Theory of Dynamical Systems
    R. van Zon, H. van Beijeren and J. R. Dorfman
    Dynamics: Models and Kinetic Methods for Non-equilibrium Many-Body Systems (J. Karkheck Ed.), NATO Sci. Ser. E Appl. Sci. 371, 131-168 (Kluwer, Dordrecht, 2000)
    [doi:10.1007/978-94-011-4365-3_8] [pdf]
  41. Chaos in Dilute Hard Sphere Gases in and out of Equilibrium
    R. van Zon
    Ph.D. thesis, Utrecht University 2000 (Shaker Publishing, The Netherlands)
    [pdf]
  42. Kinetic Approach to the Gaussian Thermostat in a Dilute Sheared Gas in the Thermodynamic Limit
    R. van Zon
    Physical Review E 60, 4158-4163 (1999)
    [doi:10.1103/PhysRevE.60.4158] [pdf]
  43. Largest Lyapunov Exponent for Many Particle Systems at Low Densities
    R. van Zon, H. van Beijeren and Ch. Dellago
    Physical Review Letters 80, 2035-2038 (1998)
    [doi:10.1103/PhysRevLett.80.2035] [pdf]
  44. The Elliptical Billiard: Subtleties of Separability
    R. van Zon and Th. W. Ruijgrok
    European Journal of Physics 19, 77-84 (1998)
    [doi:10.1088/0143-0807/19/1/011] [pdf]
  45. The Elliptical Billiard
    R. van Zon
    Unpublished M.Sc. thesis, Utrecht University (1996)
    [pdf]